Regulation Of Immune-related Genes Research Articles

Integrative study of chicken lung transcriptome to understand the host immune response during Newcastle disease virus challenge.

Newcastle disease is one of the significant issues in the poultry industry, having catastrophic effects worldwide. The lung is one of the essential organs which harbours Bronchus-associated lymphoid tissue and plays a vital role in the immune response. Leghorn and Fayoumi breeds are known to have differences in resistance to Newcastle disease. Along with genes and long non-coding RNAs (lncRNAs) are also known to regulate various biological pathways through gene regulation. This study analysed the lung transcriptome data and identified the role of genes and long non-coding RNAs in differential immune resistance. The computational pipeline, FHSpipe, as used in our previous studies on analysis of harderian gland and trachea transcriptome was used to identify genes and lncRNAs. This was followed by differential expression analysis, functional annotation of genes and lncRNAs, identification of transcription factors, microRNAs and finally validation using qRT-PCR. A total of 8219 novel lncRNAs were identified. Of them, 1263 lncRNAs and 281 genes were differentially expressed. About 66 genes were annotated with either an immune-related GO term or pathway, and 12 were annotated with both. In challenge and breed-based analysis, most of these genes were upregulated in Fayoumi compared to Leghorn, and in timepoint-based analysis, Leghorn challenge chicken showed downregulation between time points. A similar trend was observed in the expression of lncRNAs. Co-expression analysis has revealed several lncRNAs co-expressing with immune genes with a positive correlation. Several genes annotated with non-immune pathways, including metabolism, signal transduction, transport of small molecules, extracellular matrix organization, developmental biology and cellular processes, were also impacted. With this, we can understand that Fayoumi chicken showed upregulated immune genes and positive cis-lncRNAs during both the non-challenged and NDV-challenge conditions, even without viral transcripts in the tissue. This finding shows that these immune-annotated genes and coexpressing cis-lncRNAs play a significant role in Fayoumi being comparatively resistant to NDV compared to Leghorn. Our study affirms and expands upon the outcomes of previous studies and highlights the crucial role of lncRNAs during the immune response to NDV. This analysis clearly shows the differences in the gene expression patterns and lncRNA co-expression with the genes between Leghorn and Fayoumi, indicating that the lncRNAs and co-expressing genes might potentially have a role in differentiating these breeds. We hypothesise that these genes and lncRNAs play a vital role in the higher resistance of Fayoumi to NDV than Leghorn. This study can pave the way for future studies to unravel the biological mechanism behind the regulation of immune-related genes.

Immobilization antigens provide orange-spotted grouper (Epinephelus coioides) protection against Cryptocaryon irritans infection

Vaccination is a way to prevent Cryptocaryon irritans outbreaks and immobilization antigens (I-antigens) are considered for vaccine development against the parasite.However, the information of C. irritans I-antigens is limit. In this study, we characterized three immobilization antigen genes (CI-IA1, CI-IA2, and CI-IA8) from C. irritans. All three I-antigens contain signal peptides, transmembrane domains, and a GPI anchor. Conserved antigenic epitope sites were found in the I-antigens sequences. After removing signal peptides and transmembrane domains, the codons of truncated I-antigens were optimized and expressed in Escherichia coli. The purified recombinant I-antigens were recognized by grouper anti-serum generated by surface exposure or intraperitoneal injection with theronts, indicating that the recombinant I-antigens have immunogenicity. After intraperitoneal injection with recombinant I-antigens, it was found that vaccination with CI-IA1, CI-IA2, and CI-IA8 generated higher immobilization titer and protected grouper against C. irritans infection. The parasite reduced the rate of Ci-IA1, CI-IA2, and CI-IA8 by 25.55%, 17.13%, and 21.05%, respectively. Higher specific IgM antibody titers were detected in serum and mucus from the vaccine group. The regulation of immune-related genes after the vaccination was determined and showed that the adaptive immune response was active during the immunization. These findings suggested that vaccination with recombinant Ci-IA1, CI-IA2, and CI-IA8 elicits protective immunity in grouper against C. irritans and those I-antigens may serve as a potential antigen for vaccine development.

The LINC00261/MiR105-5p/SELL axis is involved in dysfunction of B cell and is associated with overall survival in hepatocellular carcinoma.

BackgroundPrevious studies have been reported the immune dysfunction of various live tissues. However, the potential molecular mechanism of post-transcriptional regulation of immune related genes in hepatocellular carcinoma (HCC) is still not clear. We tried to identify crucial immune related biomarkers associated with HCC patients’ outcomes and to reveal the transcriptional regulation.MethodThe fractions of 22 immune cells in tumor and adjacent tissues were estimated by CIBERSORT. Kruskal-Wallis test and differentially expressed analyzes were used for comparative studies. Cox proportional hazard regression model, Kaplan-Meier estimates and Log-rank test were used for survival analyses.ResultsFrom The Cancer Genome Atlas (TCGA), the gene, lncRNA and miRNA expression profiles of 379 HCC samples with clinical information were used for comparative studies. Eleven adaptive and innate immune cell types were significantly altered in HCC samples, including B cell memory, regulatory T cells and follicular helper T cells. Differentially expressed competing endogenous RNA (ceRNA) network associated with patients’ overall survival was identified. Then, the novel pathway, including LINC00261, MiR105-5p and selectin L(SELL) was found and may be potential novel biomarkers for patients’ outcomes and immunotherapy. Furthermore, SELL was significantly positively correlated (correlation coefficients: 0.47–0.69) with 12 known gene signatures of immunotherapy except for programmed cell death 1 (PDCD1).ConclusionsOur findings could provide insights into the selection of novel LINC00261/MiR105-5p/SELL pathway which is associated with overall survival and may impact on efficacy of immunotherapy in HCC.

Evaluation of the effect of some chemicals used in the Nile tilapia (Oreochromis niloticus) culture

This study was conducted to assess genotoxic and histopathological changes induced by some chemicals applied in aquaculture as Oxytetracycline (OTC) from the antibiotics group, Malathion (MAL) from the pesticides group, or Formalin and malachite green [D1] [MF2] [MF3] FMG from disinfectants group in Nile tilapia (Oreochromis niloticus) culture as a model of toxicological studies in aquatic surroundings. Fish were exposed to OTC in a dose of 80 mg kg/biomass/day, MAL in a dose of 0.1 ppm, or FMG in a dose of 100 ppm and 0.2 ppm respectively for 21 days. The genotoxic effect was determined through DNA damage detection by comet assay as revealed a significant increase in tail length, tail DNA%, and tail moment, all chemicals revealed DNA damage when compared to control. qPCR revealed significant (p <0.05) down regulation of immunity-related genes, MHC IIA, Tlr7, and IgM heavy chain in head-kidney and significant (p <0.05) upregulation in the expression level of the inflammatory gene, TNF-α, in liver tissue of all chemicals treated groups in comparison with a control group. Histopathological examination of liver and kidney revealed hepatocyte and renal damage. [D1]Is malachite green [D1]is still applied in aquaculture in Egypt? It is banned in many countries worldwide [MF2]Used in fish hatcheries under restricted rules, and use only Zinc free malachite green [MF3]

Sphingosine Kinase 1 is Associated With Immune Cell–Related Gene Expressions in Human Breast Cancer

BackgroundAlthough previous experiments have implicated sphingosine-1-phosphate (S1P) as a links between immune reactions and cancer progression, the exact mechanism of this interaction has not comprehensively studied in clinical human samples. This study sought to evaluate the S1P regulation by sphingosine kinase 1 (SPHK1), an S1P-producing enzyme, in the immunity/immuno-reactivity of clinical human breast cancer surgical specimens. MethodsS1P levels were examined in tumor, peritumoral, and normal human breast samples using mass spectrometry. Genomics Data Commons data portal of The Cancer Genome Atlas cohort was used to assess the expression of S1P-related and immune-related genes. ResultsS1P levels were significantly higher in tumor samples compared to peritumoral (P < 0.05) or normal human breast samples (P < 0.001). SPHK1 gene expression was elevated in tumoral samples compared to normal breast samples (P < 0.01). Furthermore, the elevated expression of SPHK1 in breast cancer tissue was associated with an increased expression of the different kinds of immune-related genes, such as CD68, CD163, CD4, and FOXP3 (forkhead box P3), in HER2-negative breast cancer. Network analysis showed the central role of SPHK1 in the interaction of S1P signaling and expression of immune cell–related proteins. ConclusionsWe demonstrated that S1P is mainly produced by tumor tissue, rather than peritumoral tissue, in breast cancer patients. Our data revealed the involvement of S1P signaling in the regulation of immune-related genes, suggesting the links between S1P and complicated immune–cancer interactions in breast cancer patients.

Single molecule real-time sequencing and RNA-seq unravel the role of long non-coding and circular RNA in the regulatory network during Nile tilapia (Oreochromis niloticus) infection with Streptococcus agalactiae

BackgroundThe tilapia aquaculture industry is facing heavy economic losses due to Streptococcus agalactiae (S. agalactiae) infections. While progress has been made in past years, the lack of a high-quality tilapia genome and transcript annotations makes systematic and comprehensive exploration for a non-coding RNA regulatory network associated with the infection process unfeasible, and it stunts further research focused on disease defense and treatment. Herein, single molecular real time sequencing (SMRT-Seq) and RNA-seq data were utilized to generate a high-quality transcript annotation. In addition, Changes in mRNA and non-coding RNA expression were also analyzed during a S. agalactiae infection in tilapia. FindingsIn total, 16.79 Gb of clean data were obtained by sequencing on six SMRT cells, with 712,294 inserts (326,645 full-length non-chimeric reads and 354,188 non-full-length reads). A total of 197,952 consensus transcripts were obtained. Additionally, 55,857 transcript sequences were acquired, with 12,297 previously annotated and 43,560 newly identified transcripts. To further examine the immune response in Oreochromis niloticus following a S. agalactiae infection, a total of 470.62 Gb of clean data was generated by sequencing a library containing 18 S. agalactiae infected tilapia samples. Of the identified genes, 9911 were newly exploited, of which 7102 were functional annotated. Furthermore, 7874 mRNAs, 1281 long non-coding RNAs (out of 21,860 long non-coding RNAs), and 61 circular RNAs (out of 1026 circular RNAs) were found to be differentially expressed during infection, with the 1026 circRNAs not previously identified in tilapia. Moreover, k-means clustering and WGCNA analyses revealed that the immune response of tilapia to a S. agalactiae infection can be divided into three stages: cytokines driven rapid immune response, energy metabolism promotion, and the production of lysosomes and phagosomes. During this response, the head kidney and spleen have synergistic effects, while maintaining independent characteristics. Finally, lncRNA-mRNA (trans and cis), lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA regulatory networks were constructed and revealed that non-coding RNA is involved in the regulation of immune-related genes. ConclusionsThis study generated a greatly-improved transcript annotation for tilapia using long-read PacBio sequencing technology, and revealed the presence of a regulatory network comprised of non-coding RNAs in Nile tilapia infected with S. agalactiae.

Regulation of Immunity-Related Genes by Infectious Bronchitis Virus Challenge in Spleen of Laying Chickens.

Understanding of host pathogen interactions is important in planning strategies for effective control of the pathogen. The present study investigated the regulation of genes involved in the activation of splenic immune system in mature laying chickens challenged with T strain of infectious bronchitis virus (IBV). Among all the genes studied, the relative expression levels of Fas cell surface death receptor (FAS), interleukin 7 (IL7), IL18, proteasome subunit alpha 3 (PSMA3), major histocompatibility complex, class II (MHCII), interferon alpha (IFNα), immunoglobulin A (IgA), and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) were significantly (p < 0.05) upregulated, while Toll-like receptor 7 (TLR7) and TLR5 were significantly downregulated in the challenge compared with the control group. Genes such as vascular cell adhesion molecule 1 (VCAM1), FK506-binding protein 1B (FKBP1B), transforming growth factor-beta 3 (TGFB3), NLR family pyrin domain containing 3 (NLRP3), TYRO3 protein tyrosine kinase (TYRO3), TNF receptor-associated factor 3 (TRAF3), C-X-C motif chemokine receptor 4 (CXCR4), macrophage inflammatory protein-3 (MIP3A), TLR2-1, TLR3, and TLR21 were not altered in mRNA expression levels between the challenge and control groups. In conclusion, the splenic immune response to IBV infection involved the regulation of cytokines, TLRs and NF-κB.

A Comparative Analysis of Edwardsiella tarda-Induced Transcriptome Profiles in RAW264.7 Cells Reveals New Insights into the Strategy of Bacterial Immune Evasion.

Edwardsiella tarda is a Gram-negative bacterial pathogen with a broad host range, including fish, reptiles, and mammals. One prominent virulence feature of E. tarda is its ability to survive and replicate in host phagocytes, but the relevant molecular mechanism is largely unknown. In this study, we examined the transcriptome profiles of RAW264.7 cells, a murine macrophage cell line, infected with live E. tarda or stimulated with dead E. tarda for 4 h and 8 h. Eighteen libraries were constructed, and an average of 69 million clean reads per library were obtained, with ~81.63% of the reads being successfully mapped to the reference genome. In total, 208 and 232 differentially expressed genes (DEGs) were identified between live and dead E. tarda-treated cells at 4 h and 8 h post-infection, respectively. The DEGs were markedly enriched in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with immunity. Live E. tarda differed strikingly from dead E. tarda in the regulation of immune related genes. Compared with dead E. tarda-treated cells, live E. tarda-treated cells exhibited marked and significant suppression in the induction of a large amount of immune genes, including RIG-I-like receptors, cytokines, and interferon-related genes. Furthermore, some of the immune genes highly regulated by live E. tarda formed complicated interaction networks with each other. Together, the results of this study revealed a transcriptome profile specifically induced by the active virulence elements of live E. tarda during the infection process, thus adding new insights into the intracellular infection mechanism of E. tarda. This study also provided a valuable set of target genes for further study of the immune evasion strategy of E. tarda.

Aedes aegypti HPX8C modulates immune responses against viral infection.

Mosquitoes act as vectors of numerous pathogens that cause human diseases. Dengue virus (DENV) transmitted by mosquito, Aedes aegypti, is responsible for dengue fever epidemics worldwide with a serious impact on human health. Currently, disease control mainly relies on vector targeted intervention strategies. Therefore, it is imperative to understand the molecular mechanisms underlying the innate immune response of mosquitoes against pathogens. In the present study, the expression profiles of immunity-related genes in the midgut responding to DENV infection by feeding were analyzed by transcriptome and quantitative real-time PCR. The level of Antimicrobial peptides (AMPs) increased seven days post-infection (d.p.i.), which could be induced by the Toll immune pathway. The expression of reactive oxygen species (ROS) genes, including antioxidant genes, such as HPX7, HPX8A, HPX8B, HPX8C were induced at one d.p.i. and peaked again at ten d.p.i. in the midgut. Interestingly, down-regulation of the antioxidant gene HPX8C by RNA interference led to reduction in the virus titer in the mosquito, probably due to the elevated levels of ROS. Application of a ROS inhibitor and scavenger molecules further established the role of oxygen free radicals in the modulation of the immune response to DENV infection. Overall, our comparative transcriptome analyses provide valuable information about the regulation of immunity related genes in the transmission vector in response to DENV infection. It further allows us to identify novel molecular mechanisms underlying the host-virus interaction, which might aid in the development of novel strategies to control mosquito-borne diseases.

TLR-4/microRNA-125a/NF-κB signaling modulates the immune response to Mycobacterium tuberculosis infection

ABSTRACT Tuberculosis (TB), caused by Mycobacterium tuberculosis, could lead to kinds of clinical disorders and remains a leading global health problem, resulting in great morbidity and mortality worldwide. Previous studies have firmly demonstrated that M. tuberculosis (M.tb) has evolved to utilize different mechanisms to evade or attenuate the host immune response, such as regulation of immune-related genes by modulation of miRNAs of host or bacteria. However, the knowledge of functions of miRNAs during M.tb infection remains limited. Here, we reported that a host microRNA, miR-125a, was significantly up-regulated by M.tb infection in both RAW264.7 and THP-1cells, in a TLR4 signaling-dependent manner. Subsequently, our results demonstrated that miR-125a was a negative regulator of NF-kB pathway by directly targeting TRAF6, resulting in the suppression of cytokines, attenuation of immune response and promotion of M.tb survival. Taken together, our findings provide a novel detailed molecular mechanism in which miR-125a was enhanced to inhibit inflammatory cytokines secretion and attenuate the immune response during M.tb infection in RAW264.7 and THP-1 cells, and suggest an intrinsic a promising anti-M.tb therapeutic target.

Six Tissue Transcriptomics Reveals Specific Immune Suppression in Spleen by Dietary Polyunsaturated Fatty Acids.

Dietary polyunsaturated fatty acids (PUFA) are suggested to modulate immune function, but the effects of dietary fatty acids composition on gene expression patterns in immune organs have not been fully characterized. In the current study we investigated how dietary fatty acids composition affects the total transcriptome profile, and especially, immune related genes in two immune organs, spleen (SPL) and bone marrow cells (BMC). Four tissues with metabolic function, skeletal muscle (SKM), white adipose tissue (WAT), brown adipose tissue (BAT), and liver (LIV), were investigated as a comparison. Following 8 weeks on low fat diet (LFD), high fat diet (HFD) rich in saturated fatty acids (HFD-S), or HFD rich in PUFA (HFD-P), tissue transcriptomics were analyzed by microarray and metabolic health assessed by fasting blood glucose level, HOMA-IR index, oral glucose tolerance test as well as quantification of crown-like structures in WAT. HFD-P corrected the metabolic phenotype induced by HFD-S. Interestingly, SKM and BMC were relatively inert to the diets, whereas the two adipose tissues (WAT and BAT) were mainly affected by HFD per se (both HFD-S and HFD-P). In particular, WAT gene expression was driven closer to that of the immune organs SPL and BMC by HFDs. The LIV exhibited different responses to both of the HFDs. Surprisingly, the spleen showed a major response to HFD-P (82 genes differed from LFD, mostly immune genes), while it was not affected at all by HFD-S (0 genes differed from LFD). In conclusion, the quantity and composition of dietary fatty acids affected the transcriptome in distinct manners in different organs. Remarkably, dietary PUFA, but not saturated fat, prompted a specific regulation of immune related genes in the spleen, opening the possibility that PUFA can regulate immune function by influencing gene expression in this organ.

MiR-143 induces expression of AIM2 and ASC in Jurkat cell line.

Absent in Melanoma 2 (AIM2) is an intracellular microbial dsDNA sensor which plays an important role in production of proinflammatory cytokines through Apoptosis associated Speck-like protein containing a Caspase activation and recruitment domain (ASC) and Caspase-1. Micro-RNAs (miRNAs) play important roles in regulation of immune related genes. However, there is little information regarding the effects of miRNAs on the AIM2 and ASC expression. To determine the mRNA levels of AIM2 and ASC in Jurkat cell line following introducing miRNA-143 (miR-143). MiR-143, a scrambled sequence and PBS were introduced separately, to the Jurkat cell lines and the mRNA levels of AIM2 and ASC were examined in parallel with beta-actin and GAPDH (as housekeeping genes) using Real-Time PCR technique. The mRNA levels of AIM2 and ASC were significantly increased in the miR-143 transfected Jurkat cells when compared to the scrambled sequence or PBS treated cells. miR-143 can lead to increased expression of AIM2 and ASC mRNAs. Considering the significance of AIM2 and ASC in DNA sensing and inflammosome formation, it can be considered as a therapeutic agent for the treatment of chronic infectious diseases, especially viral infections.

Regulation of prostate cancer immunity-related genes in PC3 prostate cancer cells by ETS-1

Prostate cancer (PCa) is one of the most prevalent forms of cancer affecting males worldwide, and knowledge of the immune defenses involved in PCa remains incomplete. Since the identification of immunity-related genes may have enormous implications for the understanding of PCa immunology, we recently reported the identification of immunity-related genes in PCa tissues and found potential binding sites for the ETS family prototype, ETS-1, in the majority of genes identified. Therefore, as a continuation of our previous study, we investigated whether ETS-1 regulates these genes in an in vitro PCa cell line model, PC3 cells. We specifically blocked ETS-1 in PC3 cells by transfection with an ETS-1 inverse antisense expression vector or a mock control vector. We then assessed the effect of the blockade on the expression of the recently identified PCa immunity-related genes using a comprehensive oligo gene expression microarray analysis. The results showed that ETS-1 is involved in the activation or repression of the recently identified immunity-related genes in PCa. These findings provide insights into the regulation of immunity-related genes in PCa, and emphasize the importance of ETS-1 in prostate cancer immunology.

Abstract B56: Regulation of immune-related genes by integrin signaling affects the cancer cell proliferation and invasion

Abstract Cytokines have been implicated in tumor proliferation and metastasis. Saxatillin, snake venom-derived disintegrin, is known to suppress tumor progression in vivo and in vitro but its correlation with cytokine's functions has not been known yet. We have investigated the role of immune-related genes in cancer cell proliferation and metastasis in human ovarian cancer cell (MDAH 2774). We demonstrate that saxatilin, an integrin antagonist, mitigated MDAH 2774 proliferation and invasion by reducing the level of TNF- induced matrix metalloproteinase-9 (MMP-9) and IL-8 expression in a dose-dependent manner. And Immunoblot assay of nuclear extracts of the cancer cells implicated that signal transducer and activator of transcription (STAT) is related in integrin signaling pathway. We also observed the activity of human glioma cell-invasion mediated by IL-8, as examined by a Boyden chamber assay, involved the mechanism of enhancing the actin stress fiber formation. IL-8 increased the phosphorylation of focal adhesion kinase (FAK), known to be the site of integrin clustering and nuclear translocation of STAT. We have shown here that interleukin-8 promotes the cancer proliferation and that mRNA levels of immune-related genes are regulated by disintegrin in human ovarian cancer cell line. These results demonstrate immune-related genes as a mediator of metastasis and proliferation and disintegrin would contribute in slowing of cancer development by regulating integrin signaling. (This work was supported by the Korea Science and Engineering Foundation (KOSEF) grant funded by the Korea Government (No.2009-0081759), KIST grant, and the Brain Korea 21 (BK21) program.) Citation Information: Cancer Prev Res 2010;3(1 Suppl):B56.